Colour Schemes

From 5a6d8d69732445af2189fc4bab7a09dbd77bb829 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 27 Nov 2006 14:00:26 +0000 Subject: [PATCH] 2.2 documentation --- help/html/colourSchemes/index.html | 552 ++++++++++++------------- help/html/menus/alignmentMenu.html | 788 +++++++++++++++++++----------------- help/html/menus/alwSelect.html | 5 +- help/html/menus/alwcalculate.html | 108 ++--- help/html/menus/alwview.html | 1 - help/html/menus/desktopMenu.html | 137 ++++--- help/html/menus/index.html | 35 +- help/html/menus/popupMenu.html | 231 ++++++----- 8 files changed, 973 insertions(+), 884 deletions(-) diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index 713b225..fc5e098 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -1,272 +1,280 @@ - - -Colour Schemes - - - -

Colour schemes

Jalview allows the user to set a background colour for the whole alignment - and also set the colour of defined groups within the alignment.

To change the background colour, simply select the colour from the "Colour" - menu.

To change the colour of a group, right click on any residue within a group - and use the popup menu to define the group colour.

At the top of the "Colour" menu the tick box "Apply Background - Colour to all groups". This is automatically ticked as default and means - the chosen colour will be applied to all existing groups. If you wish to maintain - the colour scheme for defined groups, make sure you deselect this option before - changing the background colour.

- -

- - - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Clustal

Zappo

Taylor

Hydrophobicity

Helix Propensity

Strand Propensity

Turn Propensity

Buried Index

- - + + +Colour Schemes + + + +

Colour schemes

Jalview allows the user to set a background colour for the whole +alignment view or for each group defined on regions within it.

To change the background colour, simply select the colour from +the "Colour" menu.

To change the colour of a group, right click on any residue +within a group and use the popup menu to define the group colour.

At the top of the "Colour" menu the tick box +"Apply Background Colour to all groups". This is ticked by +default so that a chosen colour scheme will be applied to all existing +groups. If you wish to maintain the colour scheme for defined groups, +make sure you deselect this option before changing the background +colour.

The "Colour→Colour Text..." entry +opens a dialog box to set a different text colour for light and dark +background, and the intensity threshold for transition between them.

The default colour schemes are summarised in the table below: +

+ + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Clustal

Zappo

Taylor

Hydrophobicity

Helix Propensity

Strand Propensity

Turn Propensity

Buried Index

+ + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 427ab2d..376792f 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,365 +1,423 @@ - -Alignment Window Menus - - -

Alignment Window Menus

File -
- Add Sequences
  - Add sequences to the visible alignment from file, URL, or cut & paste - window
- Fetch Sequence
  - Shows a dialog window in which you can select known ids from Uniprot, - EMBL, EMBLCDS or PDB database using Web Services provided by the European - Bioinformatics Institute. See Sequence - Fetcher.
- Save As
  - Save the alignment to local file. A file selection window - will open, use the "Files of type:" selection box to determine - which alignment format to save as.
- Export
  - Creates an alignment graphic with the current annotation, alignment background - colours and group colours. If the alignment is wrapped, the output will also be wrapped - and will have the same visible residue width as the open alignment. -
  - HTML
    - Create a web page from - your alignment.
  - EPS
    - Create an Encapsulated Postscript - file from your alignment.
  - PNG
    - Create a Portable Network - Graphics file from your alignment.
  -
- Output to Textbox
  - The alignment will be displayed in plain text in a new window - which you can "Copy and Paste" using the pull down menu, or - your standard operating system copy and paste keys.
  - Select the format of the text by selecting one of the following menu items. -
  - FASTA
  - MSF
  - CLUSTAL
  - BLC
  - PIR
  - PFAM
  -
- Print
  - Jalview will print the alignment using the current fonts - and colours of your alignment. If the alignment has annotations visible, - these will be printed below the alignment. If the alignment is wrapped - the number of residues per line of your alignment will depend on the paper - width or your alignment window width, whichever is the smaller.
- Export Features
  - All features visible on the alignment can be saved to file or displayed - in a textbox in either Jalview or GFF format
- Export Annotations
  - All annotations visible on the alignment can be saved to file or displayed - in a textbox in Jalview annotations format.
- Load Associated Tree
  - Jalview can view trees stored in the Newick - file format, and associate them with the alignment. Note: the ids of the - tree file and your alignment MUST be the same.
- Load Features / Annotations
  - Load files describing precalculated sequence - features or alignment - annotations.
- Close
  - Close the alignment window. Make sure you have saved your alignment - before you close - either as a Jalview project or by using the Save - As menu.
  -
-
Edit -
- Undo
  - This will undo any edits you make to the alignment. This applies to insertion - or deletion of gaps, cutting residues or sequences from the alignment - or pasting sequences to the current alignment or sorting the alignment. - NOTE: It DOES NOT undo colour changes, adjustments to - group sizes, or changes to the annotation panel.
- Redo
  - Any actions which you undo can be redone using redo.
- Cut
  - This will make a copy of the currently selected residues - before removing them from your alignment. Click on a sequence name if - you wish to select a whole sequence.
  - Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
- Copy
  - Copies the currently selected residues to the system clipboard - you - can also do this by pressing <CTRL> and C (<APPLE> and C on - MacOSX).
  - If you try to paste the clipboard contents to a text editor, you will - see the format of the copied residues FASTA.
- Paste -
  - To New Alignment
    - A new alignment window will be created from sequences - previously copied or cut to the system clipboard.
    - Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
  - Add To This Alignment
    - Copied sequences from another alignment window can be - added to the current Jalview alignment.
  -
- Delete
  - This will delete the currently selected residues without - copying them to the clipboard. Like the other edit operations, this can - be undone with Undo.
- Select All
  - Selects all the sequences and residues in the alignment. -
  - Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
- Deselect All
  - Removes the current selection box (red dashed box) from the - alignment window. All selected sequences, residues and marked columns - will be deselected.
  - Use <ESCAPE> to deselect all.
- Invert Sequence Selection
  - Any sequence ids currently not selected will replace the - current selection.
- Invert Column Selection
  - Any columns currently not selected will replace the current - column selection.
- Undefine Groups
  - The alignment will be reset with no defined groups.
  - WARNING: This cannot be undone.
- Remove Left
  - If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
- Remove Right
  - If the alignment has marked columns, the alignment will be - trimmed to the left of the leftmost marked column. To mark a column, mouse - click the scale bar above the alignment. Click again to unmark a column, - or select "Deselect All" to deselect all columns.
- Remove Empty Columns
  - All columns which only contain gap characters ("-", - ".") will be deleted.
  - You may set the default gap character in preferences. -
- Remove All Gaps
  - Gap characters ("-", ".") will be deleted from - the selected area of the alignment. If no selection is made, ALL the gaps - in the alignment will be removed.
  - You may set the default gap character in preferences. -
- Remove Redundancy
  - Selecting this option brings up a window asking you to select - a threshold. If the percentage identity between any two sequences (under - the current alignment) exceeds this value then one of the sequences (the - shorter) is discarded. Press the "Apply" button to remove redundant - sequences. The "Undo" button will undo the last redundancy deletion.
- Pad Gaps
  - When selected, the alignment will be kept at minimal width - (so there no empty columns before or after the first or last aligned residue) - and all sequences will be padded with gap characters to the before and - after their terminating residues.
  - This switch is useful when making a tree using unaligned sequences and - when working with alignment analysis programs which require 'properly - aligned sequences' to be all the same length.
  - You may set the default for Pad Gaps in the preferences. -
  -
-
Search -
- Find
  - Select this to search - for residues, sequence name or residue position within the alignment and - create new sequence features from the queries.
  -
-
View -
- Font
  - Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
- Smooth Fonts
  - If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
- Show (all Columns / Sequences)
  - All hidden Columns / Sequences will be revealed.
- Hide (all Columns / Sequences)
  - Hides the all the currently selected Columns / Sequences
- Wrap
  - When ticked, the alignment display is "wrapped" - to the width of the alignment window. This is useful if your alignment - has only a few sequences to view its full width at once.
  - Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each - sequence row.
  - NOTE: When in wrapped alignment view, the alignment cannot - be edited or have regions selected on it.
- Show Full Sequence ID
  - If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format NAME/START-END
- Boxes
  - If this is selected the background of a residue will be coloured using - the selected background colour. Useful if used in conjunction with "Colour - Text."
- Text
  - If this is selected the residues will be displayed using - the standard 1 character amino acid alphabet.
- Colour Text
  - If this is selected the residues will be coloured according - to the background colour associated with that residue. The colour is slightly - darker than background so the amino acid symbol remains visible.
- Show Gaps
  - When this is selected, gap characters will be displayed as - "." or "-". If unselected, then gap characters will - appear as blank spaces.
  - You may set the default gap character in preferences.
- Show Annotations
  - If this is selected the "Annotation Panel" will - be displayed below the alignment. The default setting is to display the - conservation calculation, quality calculation and consensus values as - bar charts.
- Fetch Sequence Features
  - If the sequence names are Swissprot entries Jalview will - use the names to retrieve sequence - features from the EBI. Features which are 1 residue in length are - coloured red, sequences longer than 1 residue are coloured blue. Move - the mouse over a coloured feature to display the details of the feature. -
  - Note: The retrieved information will update the sequence start and end - labels if they are incorrect.
- Show Sequence Features
  - Show or hide sequence features on this alignment.
- Seqence Feature Settings...
  - Control the colour and display of sequence features on the alignment. - See Sequence Feature Settings.
- Overview Window
  - A scaled version of the alignment will be displayed in a - small window. A red box will indicate the currently visible area of the - alignment. Move the visible region using the mouse.
-
Colour -
- Apply Colour To All Groups
  - If this is selected, any changes made to the background colour - will be applied to all currently defined groups.
- Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage - Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, - Turn Propensity, Buried Index, Nucleotide, User Defined
  - See colours for - a description of all colour schemes.
- By Conservation
  - See Colouring - by Conservation.
- Modify Conservation Threshold
  - Use this to display the conservation threshold slider window. - Useful if the window has been closed, or if the 'by conservation' option - appears to be doing nothing!
- Above Identity Threshold
  - See Above Percentage - Identity.
- Modify Identity Threshold
  - Use this to set the threshold value for colouring above Identity. - Useful if the window has been closed.
- By Annotation
  - Colours the alignment on a per-column value from a specified annotation. - See Annotation Colouring.
  -
-
Calculate -
- Sort -
  - by ID
    - This will sort the sequences according to sequence name. If the sort - is repeated, the order of the sorted sequences will be inverted.
  - by Group
    - This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be - inverted.
  - by Pairwise Identity
    - This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
  - The Sort menu will - have some additional options if you have just done a multiple alignment - calculation, or opened a tree viewer window.
  -
- Calculate Tree
  - Functions for calculating trees on the alignment or the currently - selected region. See calculating trees. -
  - Average Distance Using % Identity
  - Neighbour Joining Using % Identity
  - Average Distance Using Blosum62
  - Neighbour Joining Using Blosum62
  -
- Pairwise Alignments
  - Applies Smith and Waterman algorithm to selected sequences. See pairwise - alignments.
- Principal Component Analysis
  - Shows a spatial clustering of the sequences based on the BLOSUM62 - scores in the alignment. See Principal - Component Analysis.
- Translate cDNA
  - If you are viewing a cDNA alignment a very simple translation service - is available. The translation ignores all gaps in the cDNA sequences. -
  -
-
Web Service
- Selecting one of the following menu items starts a remote service - on compute facilities at the University of Dundee. You need a continuous network - connection in order to use these services through Jalview. -
- Alignment -
  - ClustalW Multiple Sequence Alignment
    - Submits all, or just the currently selected sequences for alignment - with clustal W.
  - ClustalW Multiple Sequence Alignment Realign
    - Submits the alignment or currently selected region for re-alignment - with clustal W. Use this if you have added some new sequences to an - existing alignment.
  - Muscle Multiple Protein Sequence Alignment
    - Submits all, or jut the currently selected sequences for alignment - using Muscle. Do not use this if you are working with nucleic acid - sequences.
  -
- Secondary Structure Prediction -
  - JPred Secondary Structure Prediction
    - Secondary structure prediction by network consensus. The behaviour - of this calculation depends on the current selection:
  - If nothing is selected, and the displayed sequences appear to - be aligned, then a JNet prediction will be run for the first sequence - in the alignment, using the current alignment. Otherwise the first - sequence will be submitted for prediction.
  - If just one sequence (or a region on one sequence) has been - selected, it will be submitted to the automatic JNet prediction server - for homolog detection and prediction.
  - If a set of sequences are selected, and they appear to be aligned, - then the alignment will be used for a Jnet prediction on the first - sequence selected in the set (that is, the one that was first clicked - on).
  -
-

- - + + +Alignment Window Menus + + + +

Alignment Window Menus

File +
- Fetch Sequence
  + Shows a dialog window in which you can select known ids from + Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by + the European Bioinformatics Institute. See Sequence Fetcher.
- Add Sequences
  + Add sequences to the visible alignment from file, URL, or cut & + paste window
- Reload
  + Reloads the alignment from the original file, if available.
  + Warning: This will delete any edits, analyses and + colourings applied since the alignment was last saved, and cannot be + undone.
- Save (Control S)
  + Saves the alignment to the file it was loaded from (if available), in + the same format, updating the original in place.
- Save As (Control Shift S)
  + Save the alignment to local file. A file selection window + will open, use the "Files of type:" selection box to + determine which alignment format to + save as.
- Output to Textbox
  + The alignment will be displayed in plain text in a new window + which you can "Copy and Paste" using the pull down menu, or + your standard operating system copy and paste keys.
  + Select the format of the text by selecting one of the following menu + items. +
  - FASTA
  - MSF
  - CLUSTAL
  - BLC
  - PIR
  - PFAM
  +
- Print (Control P)
  + Jalview will print the alignment using the current fonts and + colours of your alignment. If the alignment has annotations visible, + these will be printed below the alignment. If the alignment is wrapped + the number of residues per line of your alignment will depend on the + paper width or your alignment window width, whichever is the smaller. +
- Export Image
  + Creates an alignment graphic with the current view's annotation, + alignment background colours and group colours. If the alignment is wrapped, the output will also be + wrapped and will have the same visible residue width as the open + alignment. +
  - HTML
    + Create a web page from your + alignment.
  - EPS
    + Create an Encapsulated + Postscript file from your alignment.
  - PNG
    + Create a Portable Network + Graphics file from your alignment.
  +
- Export Features
  + All features visible on the alignment can be saved to file or + displayed in a textbox in either Jalview or GFF format
- Export Annotations
  + All annotations visible on the alignment can be saved to file or + displayed in a textbox in Jalview annotations format.
- Load Associated Tree
  + Jalview can view + trees stored in the Newick file format, and associate them with the + alignment. Note: the ids of the tree file and your alignment MUST be + the same.
- Load Features / Annotations
  + Load files describing precalculated sequence features or alignment annotations.
- Close (Control W)
  + Close the alignment window. Make sure you have saved your + alignment before you close - either as a Jalview project or by using + the Save As menu.
+
Edit +
- Undo (Control Z)
  + This will undo any edits you make to the alignment. This applies to + insertion or deletion of gaps, cutting residues or sequences from the + alignment or pasting sequences to the current alignment or sorting the + alignment. NOTE: It DOES NOT undo colour changes, + adjustments to group sizes, or changes to the annotation panel.
- Redo (Control Y)
  + Any actions which you undo can be redone using redo.
- Cut (Control X)
  + This will make a copy of the currently selected residues + before removing them from your alignment. Click on a sequence name if + you wish to select a whole sequence.
  + Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
- Copy (Control C)
  + Copies the currently selected residues to the system + clipboard - you can also do this by pressing <CTRL> and C + (<APPLE> and C on MacOSX).
  + If you try to paste the clipboard contents to a text editor, you will + see the format of the copied residues FASTA.
- Paste +
  - To New Alignment (Control Shift V)
    + A new alignment window will be created from sequences + previously copied or cut to the system clipboard.
    + Use <CTRL> and <SHIFT> and V(<APPLE> and + <SHIFT;> and and V on MacOSX) to paste.
  - Add To This Alignment (Control V)
    + Copied sequences from another alignment window can be added + to the current Jalview alignment.
  +
- Delete (Backspace)
  + This will delete the currently selected residues without + copying them to the clipboard. Like the other edit operations, this + can be undone with Undo.
- Remove Left (Control L)
  + If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, + mouse click the scale bar above the alignment. Click again to unmark a + column, or select "Deselect All" to deselect all columns.
- Remove Right (Control R)
  + If the alignment has marked columns, the alignment will be + trimmed to the left of the leftmost marked column. To mark a column, + mouse click the scale bar above the alignment. Click again to unmark a + column, or select "Deselect All" to deselect all columns.
- Remove Empty Columns (Control E)
  + All columns which only contain gap characters ("-", + ".") will be deleted.
  + You may set the default gap character in preferences.
- Remove All Gaps (Control Shift E)
  + Gap characters ("-", ".") will be deleted + from the selected area of the alignment. If no selection is made, ALL + the gaps in the alignment will be removed.
  + You may set the default gap character in preferences.
- Remove Redundancy (Control D)
  + Selecting this option brings up a window asking you to select + a threshold. If the percentage identity between any two sequences + (under the current alignment) exceeds this value then one of the + sequences (the shorter) is discarded. Press the "Apply" + button to remove redundant sequences. The "Undo" button will + undo the last redundancy deletion.
- Pad Gaps
  + When selected, the alignment will be kept at minimal width + (so there no empty columns before or after the first or last aligned + residue) and all sequences will be padded with gap characters to the + before and after their terminating residues.
  + This switch is useful when making a tree using unaligned sequences and + when working with alignment analysis programs which require 'properly + aligned sequences' to be all the same length.
  + You may set the default for Pad Gaps in the preferences.
+
Select +
- Find... + (Control F)
  + Opens the Find dialog box to search for residues, sequence name or + residue position within the alignment and create new sequence features + from the queries.
- Select All (Control A)
  + Selects all the sequences and residues in the alignment.
  + Use <CTRL> and A (<APPLE> and A on a MacOSX) to select + all.
- Deselect All (Escape)
  + Removes the current selection box (red dashed box) from the + alignment window. All selected sequences, residues and marked columns + will be deselected.
  + Use <ESCAPE> to deselect all.
- Invert Sequence Selection (Control I)
  + Any sequence ids currently not selected will replace the + current selection.
- Invert Column Selection (Control Alt I)
  + Any columns currently not selected will replace the current + column selection.
- Undefine Groups (Control U)
  + The alignment will be reset with no defined groups.
  + WARNING: This cannot be undone.
+
View +
- New View (Control T)
  + Creates a new view from the current alignment view.
- Expand Views (X)
  + Display each view associated with the alignment in its own alignment + window, allowing several views to be displayed simultaneously.
- Gather Views (G)
  + Each view associated with the alignment will be displayed within its + own tab on the current alignment window.
- Show→(all Columns / Sequences)
  + All hidden Columns / Sequences will be revealed.
- Hide→(all Columns / Sequences)
  + Hides the all the currently selected Columns / Sequences
- Show Annotations
  + If this is selected the "Annotation Panel" will be + displayed below the alignment. The default setting is to display the + conservation calculation, quality calculation and consensus values as + bar charts.
- Show Sequence Features
  + Show or hide sequence features on this alignment.
- Seqence + Feature Settings...
  + Opens the Sequence Feature Settings dialog box to control the + colour and display of sequence features on the alignment, and + configure and retrieve features from DAS annotation servers.
+

+
Alignment Window Format Menu +
+
Font...
+ Opens the "Choose Font" dialog box, in order to + change the font of the display and enable or disable 'smooth fonts' + (anti-aliasing) for faster alignment rendering.
+
Wrap
+ When ticked, the alignment display is "wrapped" to the width of the + alignment window. This is useful if your alignment has only a few + sequences to view its full width at once.
+ Additional options for display of sequence numbering and scales are + also visible in wrapped layout mode:
+
+
Scale Above
+ Show the alignment column position scale.
+
Scale Left
+ Show the sequence position for the first aligned residue in each row + in the left column of the alignment.
+
Scale Right
+ Show the sequence position for the last aligned residue in each row + in the right-most column of the alignment.
+ +
Show Sequence Limits
+ If this box is selected the sequence name will have the start + and end position of the sequence appended to the name, in the format + NAME/START-END
+
Right Align Sequence ID
+ If this box is selected then the sequence names displayed in + the sequence label area will be aligned against the left-hand edge of + the alignment display, rather than the left-hand edge of the alignment + window.
+
Show Hidden Markers
+ When this box is selected, positions in the alignment where + rows and columns are hidden will be marked by blue arrows.
+
Boxes
+ If this is selected the background of a residue will be coloured using + the selected background colour. Useful if used in conjunction with + "Colour Text."
+
Text
+ If this is selected the residues will be displayed using the + standard 1 character amino acid alphabet.
+
Colour Text
+ If this is selected the residues will be coloured according + to the background colour associated with that residue. The colour is + slightly darker than background so the amino acid symbol remains + visible.
+
Show Gaps
+ When this is selected, gap characters will be displayed as + "." or "-". If unselected, then gap characters + will appear as blank spaces.
+ You may set the default gap character in preferences.
+
+
+
Colour +
+
Apply Colour To All Groups
+ If this is selected, any changes made to the background + colour will be applied to all currently defined groups.
+
+
Colour + Text...
+ Opens the Colour Text dialog box to set a different text colour for + light and dark background, and the intensity threshold for transition + between them.
+
Colour Scheme options: None, ClustalX, + Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, + Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, + Nucleotide, User Defined
+ See colours for a + description of all colour schemes.
+
+
By Conservation
+ See Colouring + by Conservation.
+
+
Modify Conservation Threshold
+ Use this to display the conservation threshold slider window. + Useful if the window has been closed, or if the 'by conservation' + option appears to be doing nothing!
+
+
Above Identity Threshold
+ See Above + Percentage Identity.
+
+
Modify Identity Threshold
+ Use this to set the threshold value for colouring above + Identity. Useful if the window has been closed.
+
+
By Annotation
+ Colours the alignment on a per-column value from a specified + annotation. See Annotation + Colouring.
+
+
+
+
Calculate +
+
Sort +
+
by ID
+ This will sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be inverted.
+
by Group
+ This will sort the sequences according to sequence name. If + the sort is repeated, the order of the sorted sequences will be + inverted.
+
by Pairwise Identity
+ This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put + at the top.
+
The Sort + menu will have some additional options if you have just done a + multiple alignment calculation, or opened a tree viewer window.
+
+
+
+
Calculate Tree
+ Functions for calculating trees on the alignment or the + currently selected region. See calculating + trees. +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
+
Pairwise Alignments
+ Applies Smith and Waterman algorithm to selected sequences. + See pairwise alignments.
+
+
Principal Component Analysis
+ Shows a spatial clustering of the sequences based on the + BLOSUM62 scores in the alignment. See Principal Component Analysis.
+
+
Autocalculate Consensus
+ For large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This prevents the + sometimes lengthy calculations performed after each sequence edit.
+
+
+
+
Web Service
+ Selecting one of the following menu items starts a remote + service on compute facilities at the University of Dundee. You need a + continuous network connection in order to use these services through + Jalview. +
+
Alignment +
+
ClustalW Multiple Sequence Alignment
+ Submits all, or just the currently selected sequences for + alignment with clustal W.
+
ClustalW Multiple Sequence Alignment + Realign
+ Submits the alignment or currently selected region for + re-alignment with clustal W. Use this if you have added some new + sequences to an existing alignment.
+
MAFFT Multiple Sequence Alignment
+ Submits all, or just the currently selected region for + alignment with MAFFT.
+
Muscle Multiple Protein Sequence Alignment
+ Submits all, or just the currently selected sequences for + alignment using Muscle. Do not use this if you are working with + nucleic acid sequences.
+
+
+
Secondary Structure Prediction +
+
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. The + behaviour of this calculation depends on the current selection:
+
If nothing is selected, and the displayed sequences + appear to be aligned, then a JNet prediction will be run for the + first sequence in the alignment, using the current alignment. + Otherwise the first sequence will be submitted for prediction.
+
If just one sequence (or a region on one sequence) + has been selected, it will be submitted to the automatic JNet + prediction server for homolog detection and prediction.
+
If a set of sequences are selected, and they appear + to be aligned, then the alignment will be used for a Jnet prediction + on the first sequence in the set (that is, the one + that appears first in the alignment window).
+
+
+
+
+
+ + diff --git a/help/html/menus/alwSelect.html b/help/html/menus/alwSelect.html index 87b0a49..7c5085a 100644 --- a/help/html/menus/alwSelect.html +++ b/help/html/menus/alwSelect.html @@ -7,8 +7,9 @@ Alignment Window Menus

Find... (Control F)
- Opens the Find dialog box to perform regular expression searches on the - aligned sequences and their IDs and create new features. + Opens the Find dialog box to search for residues, sequence name or + residue position within the alignment and create new sequence features + from the queries.
Select All (Control A)
Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index ed5de39..9d40868 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -1,54 +1,54 @@ - -Alignment Window Menus - - -
Alignment Window Calculate Menu
-
-
Sort -
-
by ID
- This will sort the sequences according to sequence name. If the sort is - repeated, the order of the sorted sequences will be inverted.
-
by Group
- This will sort the sequences according to sequence name. - If the sort is repeated, the order of the sorted sequences will be inverted. -
-
by Pairwise Identity
- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put at - the top.
-
The Sort menu will have - some additional options if you have just done a multiple alignment calculation, - or opened a tree viewer window.
-
-
-
-
Calculate Tree
- Functions for calculating trees on the alignment or the currently selected - region. See calculating trees. -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
-
-
-
-
Pairwise Alignments
- Applies Smith and Waterman algorithm to selected sequences. See pairwise - alignments.
-
-
Principal Component Analysis
- Shows a spatial clustering of the sequences based on the BLOSUM62 scores - in the alignment. See Principal Component - Analysis.
-
-
Autocalculate Consensus
- For large alignments it can be useful to deselect "Autocalculate - Consensus" when editing. This prevents lengthy calculations which are - performed after each sequence edit.
-
-
- - + +Alignment Window Menus + + +
Alignment Window Calculate Menu
+
+
Sort +
+
by ID
+ This will sort the sequences according to sequence name. If the sort is + repeated, the order of the sorted sequences will be inverted.
+
by Group
+ This will sort the sequences according to sequence name. + If the sort is repeated, the order of the sorted sequences will be inverted. +
+
by Pairwise Identity
+ This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put at + the top.
+
The Sort menu will have + some additional options if you have just done a multiple alignment calculation, + or opened a tree viewer window.
+
+
+
+
Calculate Tree
+ Functions for calculating trees on the alignment or the currently selected + region. See calculating trees. +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
+
Pairwise Alignments
+ Applies Smith and Waterman algorithm to selected sequences. See pairwise + alignments.
+
+
Principal Component Analysis
+ Shows a spatial clustering of the sequences based on the BLOSUM62 scores + in the alignment. See Principal Component + Analysis.
+
+
Autocalculate Consensus
+ For large alignments it can be useful to deselect "Autocalculate + Consensus" when editing. This prevents the sometimes lengthy calculations + performed after each sequence edit.
+
+
+ + diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index ca8f81b..2d341fa 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -35,7 +35,6 @@ A scaled version of the alignment will be displayed in a small window. A red box will indicate the currently visible area of the alignment. Move the visible region using the mouse. -

diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index c99b64c..7dd7b40 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -1,63 +1,74 @@ - -Desktop Menus - - -
Desktop Menus
-
-
File -
-
Input Alignment from (See more on file - formats) -
-
File
- open file(s) on your local file system
-
URL
- open a file from a website. The URL MUST start with http://
-
Textbox
- copy and paste an alignment into a text window
-
-
-
Fetch Sequence
- Shows a dialog window in which you can select known ids from - Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by - the European Bioinformatics Institute.
-
Save Project
- Saves all currently open alignment windows with their current view - settings and any associated trees, as a Jalview - Archive (which has a .jar extension).
-
Load Project
- Loads Jalview archives only.
-
Quit
- Close Jalview. Warning - any annotations you have made on alignments - will be lost unless you Save your work before quitting.
-
-
-
-
Tools -
-
Preferences
- Change the default visual settings for opening new alignment - windows.
-
-
-
-
Help -
-
About
- Displays the version and creation date of the application, - as well as acknowledgements and a citation reference.
-
Documentation
- Displays help files as a browseable, searchable set of pages - with a table of contents.
-
-
-
-
Window
- Each time a new window is added to the Jalview Desktop a new - menu item will be added to the "Window" menu. If you are working - with several alignments, trees or other types of windows use the "Window" - menu to bring your window of choice to the top of the pile if it has been - hidden by other windows.
-
- - + + +Desktop Menus + + + +
Desktop Menus
+
+
File +
+
Input Alignment from (See more on file formats) +
+
File (Control O)
+ open file(s) on your local file system
+
URL
+ open a file from a website. The URL MUST start with http://
+
Textbox
+ copy and paste an alignment into a text window
+
+
+
Fetch Sequence
+ Shows a dialog window in which you can select known ids from + Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by + the European Bioinformatics Institute.
+
Save Project
+ Saves all currently open alignment windows with their current + view settings and any associated trees, as a Jalview Archive (which has a + .jar extension).
+
Load Project
+ Loads Jalview archives only.
+
Quit
+ Close Jalview.
Note - any annotation you have made on + alignments will be lost unless you Save your work before quitting.

+
+
+
+
Tools +
+
Preferences
+ Change the default visual settings for opening new alignment + windows.
+
+
+
+
Help +
+
About
+ Displays the version and creation date of the application, as + well as acknowledgements and a citation reference.
+
Documentation
+ Displays help files as a browseable, searchable set of pages + with a table of contents.
+
+
+
+
Window
+ Each time a new window is added to the Jalview Desktop a + corresponding menu item will be added to the "Window" menu + that will bring the window to the top of the pile when it is selected. +
+
Close All
+ Close all alignment and analysis windows.
Note: This will erase all alignments from memory, and cannot be undone!
+
Raise Associated Windows
+ Bring all windows associated with the current alignment to the top of the pile. +
+
Minimise Associated Windows
+ Hide all windows related to the current alignment behind icons on the Jalview Desktop. +
+
+
+ + diff --git a/help/html/menus/index.html b/help/html/menus/index.html index 4949e87..03d764a 100755 --- a/help/html/menus/index.html +++ b/help/html/menus/index.html @@ -1,17 +1,18 @@ - -Menus - - -
Menus
-
Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment - Menu" and the "Popup Menu".
-
The Desktop Menu is always visible and is the - starting point for loading new alignments.
-
The Alignment Menu is visible once and alignment - has been opened.
-
The Popup Menu is made visible by clicking with - the right mouse button on a sequence or the name of a sequence in an alignment - window.
- - - + +Menus + + +
Menus
+
Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment + Menu" and the "Popup Menu".
+
The Desktop Menu is always visible and is the + starting point for loading new alignments.
+
The Alignment Menu is visible once and alignment + has been opened.
+
The Popup Menu is made visible by clicking with + the right mouse button on a sequence or the name of a sequence in an alignment + window.
+
The Annotations Menu is opened by right-clicking on an annotation row label.
+ + + diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 734cdc5..f885bd8 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,110 +1,121 @@ - -Popup Menu - - -
Popup Menu
- This menu is visible when right clicking either within a selected region - on the alignment or on a selected sequence name. It may not be - accessible when in 'Cursor Mode' (toggled with the F2 key).
-
-
Selection -
-
Edit -
-
Copy
- Copys the selected region. In the applet version, the copied sequences - are not available to the system clipboard.
-
Cut
- Cuts the selected region from the alignment. In the applet - version, the copied sequences are not available to the system clipboard. -
-
To Upper Case
- Changes the case of selected region to lower case. -
-
To Lower Case
- Changes the case of selected region to upper case. -
-
Toggle Case
- Switches the case of all residues within the selected region. -
-
-
-
Output to Textbox
- The selection area will be output to a a text window in the - selected alignment format.
-
Group
- This will display a window asking for the name of the currently - selected group. Click OK to set the name, cancel to use the default group - name.
-
Remove Group
- This will undefine the selected group.
-
Group Colour
- Sets the colour - of the group.
-
Boxes
- If selected the background of a residue within the selected - group will be coloured according to the assigned colour scheme. -
-
Text
- If selected the selected group will display text.
-
Colour Text
- If selected the selected group will display text in a colour - slightly darker than the background colour of that residue.
-
Border Colour
- Selecting this will display a "Colour Chooser" - window. Select a colour than press OK to set the border colour of a group.
-
-
-
-
Sequence Id
- This menu is only visible if you right-click on a sequence name. - -
-
Edit Name/Description
- You may edit the name and description of each sequence. A - window will be displayed asking for a new sequence name and sequence description - to be entered. Press OK to accept your edit. To save sequence descriptions, - you must save in Fasta, PIR or Jalview File format.
-
Associate Structure with Sequence -
-
From File
- Load a PDB file from local disk which will be associated - with this sequence. This file will be used if the user subsequently - clicks on "View PDB Structure" menu item.
-
Enter PDB id
- Enter the PDB id from an input window. This PDB id will - be used by the service WSDBFetch, provided by the EBI, to fetch the - PDB file if the user subsequently clicks on "View PDB Structure" - menu item.
-
Discover PDB ids
- This will use the service WSDBFetch, provided by the - EBI, to retrieve all PDB ids associated with the sequences in the - alignment if the sequences have valid Uniprot names or accession ids. -
-
-
-
View PDB Structure
- If the sequence has an associated PDB file added by one - of the methods described above, Jalview will display a 3D interactive - viewer of the file.
- This entry is only present if the sequence has an associated - PDB structure.
-
Represent Group With (Sequence Id)
- All sequences in the current selection group will be hidden, apart - from (Sequence Id). Any edits performed on the visible representative - sequence will be propagated to the hidden sequences.
-
Link
- This menu item lists all links which have been set up in the Preferences - Connections tab.
-
-
-
-
Hide Sequences
- This menu item lists all links which have been set up in the Preferences - Connections tab. It is only displayed when you right click (Apple click) on - a sequence id.
-
-
-
- - + + +Popup Menu + + + +
Popup Menu
+This menu is visible when right clicking either within a +selected region on the alignment or on a selected sequence name. It may +not be accessible when in 'Cursor Mode' (toggled with the F2 key).
+
+
Selection +
+
Edit +
+
Copy
+ Copys the selected region. In the applet version, the copied + sequences are not available to the system clipboard.
+
Cut
+ Cuts the selected region from the alignment. In the applet + version, the copied sequences are not available to the system + clipboard.
+
To Upper Case
+ Changes the case of selected region to lower case.
+
To Lower Case
+ Changes the case of selected region to upper case. +
+
Toggle Case
+ Switches the case of all residues within the selected + region.
+
+
+
Output to Textbox
+ The selection area will be output to a a text window in the + selected alignment format.
+
Create + Sequence Feature...
+ Opens the dialog box for creating sequence features over the + currently selected region on each selected sequence.
+
Group
+ Group Operations +
+
GroupThis will display a window + asking for the name of the currently selected group. Click OK to set + the name, cancel to use the default group name.
+
Remove Group
+ This will undefine the selected group.
+
Group Colour
+ Sets the colour of + the group.
+
Boxes
+ If selected the background of a residue within the selected + group will be coloured according to the assigned colour scheme. +
+
Text
+ If selected the selected group will display text.
+
Colour Text
+ If selected the selected group will display text in a colour + slightly darker than the background colour of that residue.
+
Border Colour
+ Selecting this will display a "Colour Chooser" + window. Select a colour than press OK to set the border colour of a + group.
+
+
+
+
+
Sequence Id
+ This menu is only visible if you right-click on a sequence + name. +
+
Edit Name/Description
+ You may edit the name and description of each sequence. A + window will be displayed asking for a new sequence name and sequence + description to be entered. Press OK to accept your edit. To save + sequence descriptions, you must save in Fasta, PIR or Jalview File + format.
+
Associate Structure with Sequence +
+
From File
+ Load a PDB file from local disk which will be associated + with this sequence. This file will be used if the user subsequently + clicks on "View PDB Structure" menu item.
+
Enter PDB id
+ Enter the PDB id from an input window. This PDB id will be + used by the service WSDBFetch, provided by the EBI, to fetch the PDB + file if the user subsequently clicks on "View PDB + Structure" menu item.
+
Discover PDB ids
+ This will use the service WSDBFetch, provided by the EBI, to + retrieve all PDB ids associated with the sequences in the alignment + if the sequences have valid Uniprot names or accession ids.
+
+
+
View PDB Structure
+ If the sequence has an associated PDB file added by one of + the methods described above, Jalview will display a 3D interactive + viewer of the file.
+ This entry is only present if the sequence has an associated PDB structure.
+
Represent Group With (Sequence Id)
+ All sequences in the current selection group will be hidden, + apart from (Sequence Id). Any edits performed on the visible + representative sequence will be propagated to the hidden sequences.
+
Link
+ This menu item lists all links which have been set up in the + Preferences Connections + tab.
+
+
+
+
Hide Sequences
+ This menu item lists all links which have been set up in the Preferences Connections tab. + It is only displayed when you right click (Apple click) on a sequence + id.
+
+
+
+ + -- 1.7.10.2